Symbiosis-EU

Abstract

Description:The current practice to assure the safety of meat still relies heavily on regulatory inspection and sampling regimes. This approach, however, seems inadequate because it cannot sufficiently guarantee consumer protection since 100% inspection and sampling is technically, financially and logistically impossible. There is a urgent need for safety and spoilage indicators to be applied in rapid analytical methods or tools for quantification to be used by meat industry as also inspection authorities need reliable methods for control purposes.

Research objectives:The overall aim of FP7 SYMBIOSIS-EU project is to identify and quantitatively evaluate practical and easy to use chemical, biochemical and molecular indices and establish their applicability as quality monitors for inspection of meat safety and quality. The project will apply a multidisciplinary system wide approach relying on converging technologies (bioinformatics, nanotechnology, modeling) to obtain knowledge for meat safety that will be translated into simple devices and practical indicators of quality and safety.

Results and products:RIKILT is WP leader of WP6: In this workpackage initially gene expression will be examined of different samples taken during the growth of P. fluorescens and/or P. putida in broth under aerobic conditions at different temperatures starting with 10 °C. The Agricultural University of Athens (AUA) has started to determined the growth curves for P. fluorescens and P. putida under these conditions and will provide RIKILT with either cells, RNA or cDNA depending on what is most convenient. Samples will be taken from late log, early stationary, mid stationary and late stationary fase. During growth additional parameters such as pH, glucose concentration, production of end-products (proteolysis may be included also) will also be monitored to provide a broader 'picture' of the environmental expression. RIKILT has checked for commercially available microarrays for P. fluorescens and P. putida and literature is currently being checked for key genes involved in spoilage metabolite production among Pseudomonads and will be continued for the next period. Futhermore RIKILT did an extensive comparative search of the available genome sequences of the Pseudomonads of interest; i.e. P. fluorescens PfO-1, P. fluorescens Pf-5, P. putida F1, P. putida GB-1, P. putida KT2440, and P. putida W619. Genes have been categorized according to primary function based on the Cluster of Orthologous Groups (COG). Additional, alignments were made for various genes after blast searches and retrieval of the DNA sequences from the public databases. The outcome of this categorization, blast and literature searches revealed that the genus Pseudomonas is very heterogeneous. Moreover, a rather large genomic diversity within the species P. fluorescens was observed, like also among the 4 P. putida strain analyzed. Additionaly, some genes/orthologs are even completely absent in either fluorescens or putida. Although, other genes are only missing in one of the available fluorescens and putida genome sequences. This inherent heterogeneity of the P. fluorescens and P. putida grouping will have to be taken in to account during the hybridizations of the microarray platforms derived from strain KT2440 or PfO-1 with non-sequenced Pseudomonas strains.